Sol Genomics Network Research Articles

Uncovering tomato candidate genes associated with drought tolerance using Solanum pennellii introgression lines.

Tomato plants are sensitive to drought stress throughout their growth cycle. To be considered drought-tolerant, a cultivar should display tolerance at all developmental stages. This study aimed to evaluate whether Solanum pennellii introgression lines (ILs) previously selected as drought-tolerant during germination/seedling growth maintained this tolerance in the vegetative/reproductive stage. We then investigated these ILs to uncover candidate genes. The plants were subjected to two different environmental conditions: well-watered and drought-stressed (water withheld for ≤ 20 d after flowering). Phenotyping for morphological, physiological, fruit quality, and yield-related traits was performed, and the data was analyzed using a mixed-model approach. Using a multi-trait index that relies on factor analysis and genotype-ideotype distance (FAI-BLUP index), the genotypes were ordered based on how far they were from the drought-tolerant ideotype. Afterward, the tomato IL population map furnished by the SOL Genomics Network was utilized to identify introgressed segments of significance for the identification of candidate genes. Significant genotypic differences were found in the yield, water content, mean weight, length, and width of the fruit, the percentage of fruits displaying blossom-end rot, and titratable acidity. The drought-tolerance ideotype was built considering the maximum values for the fruit water content, number of fruits, mean fruit weight, and yield, minimum values for blossom-end rot, and mean values for titratable acidity. IL 1-4-18, IL 7-4-1, IL 7-1, IL 7-5-5, and IL 1-2 were ranked above M-82 and therefore considered drought-tolerant during the vegetative/reproductive stage. IL 1-4-18 and IL1-2 sustained drought tolerance displayed during germination/seedling growth into the vegetative/reproductive stage. The following candidate genes associated with drought tolerance were identified: AHG2, At1g55840, PRXIIF, SAP5, REF4-RELATED 1, PRXQ, CFS1, LCD, CCD1, and SCS. Because they are already associated with genetic markers, they can be transferred to elite tomato cultivars through marker-assisted technology after validation.

Uncovering tomato candidate genes for seed germination performance and seedling vigour using the Solanum pennellii introgression line population

Both fast seed germination and seedling vigour are important for proper crop establishment and higher yields. These traits seem to be controlled by several QTL’s and are highly influenced by environmental conditions. In this work, we aimed to evaluate seed germination performance and vigour traits of several Solanum pennellii introgression lines (IL’s) to select ideotypes for germination and vigour; and then investigate the selected IL’s to uncover candidate genes for these traits. We performed a germination test followed by the analysis of seedling growth in a collection of 46 different homozygous tomato IL’s and their genitors' accession LA716 and cv M82, grown in the field in two consecutive growing seasons. From these tests, several traits were calculated. Then, we used a multi-trait index based on factor analysis and genotype-ideotype distance (FAI-BLUP index) to properly rank the genotypes according to their seed germination performance and seedling vigour. Following the ranking, introgressed segments of interest were identified for further analysis of candidate gene identification using the map of the tomato IL population as provided by the SOL Genomics Network. The IL 6−1, IL 4−1−1, IL 4−4, IL 11−4−1, IL 1−1−2, and IL 10−1 were selected through the FAI-BLUP index as the closest to the ideotype for seed germination performance and vigour. The genes At1g75350, At2g26350, At2g28490, At3g10920, At5g13200, At5g41480, and At4g21800 were identified as candidate genes for seed germination. The genes At5g53000, At1g46480, At1g30755, At5g47390, At2g29630, and At4g03400 were identified as candidate genes for seed vigour. Fine mapping, validation, and further investigation of these genes will provide valuable insights into the genetics of seed quality.

Linked Data Platform for Solanaceae Species

Genetics research is increasingly focusing on mining fully sequenced genomes and their annotations to identify the causal genes associated with traits (phenotypes) of interest. However, a complex trait is typically associated with multiple quantitative trait loci (QTLs), each comprising many genes, that can positively or negatively affect the trait of interest. To help breeders in ranking candidate genes, we developed an analytical platform called pbg-ld that provides semantically integrated geno- and phenotypic data on Solanaceae species. This platform combines both unstructured data from scientific literature and structured data from publicly available biological databases using the Linked Data approach. In particular, QTLs were extracted from tables of full-text articles from the Europe PubMed Central (PMC) repository using QTLTableMiner++ (QTM), while the genomic annotations were obtained from the Sol Genomics Network (SGN), UniProt and Ensembl Plants databases. These datasets were transformed into Linked Data graphs, which include cross-references to many other relevant databases such as Gramene, Plant Reactome, InterPro and KEGG Orthology (KO). Users can query and analyze the integrated data through a web interface or programmatically via the SPARQL and RESTful services (APIs). We illustrate the usability of pbg-ld by querying genome annotations, by comparing genome graphs, and by two biological use cases in Jupyter Notebooks. In the first use case, we performed a comparative genomics study using pbg-ld to compare the difference in the genetic mechanism underlying tomato fruit shape and potato tuber shape. In the second use case, we developed a seamlessly integrated workflow that uses genomic data from pbg-ld knowledge graphs and prioritization pipelines to predict candidate genes within QTL regions for metabolic traits of tomato.

Metabolic networks of the Nicotiana genus in the spotlight: content, progress and outlook.

Manually curated metabolic databases residing at the Sol Genomics Network comprise two taxon-specific databases for the Solanaceae family, i.e. SolanaCyc and the genus Nicotiana, i.e. NicotianaCyc as well as six species-specific databases for Nicotiana tabacum TN90, N. tabacum K326, Nicotiana benthamiana, N. sylvestris, N. tomentosiformis and N. attenuata. New pathways were created through the extraction, examination and verification of related data from the literature and the aid of external database guided by an expert-led curation process. Here we describe the curation progress that has been achieved in these databases since the first release version 1.0 in 2016, the curation flow and the curation process using the example metabolic pathway for cholesterol in plants. The current content of our databases comprises 266 pathways and 36 superpathways in SolanaCyc and 143 pathways plus 21 superpathways in NicotianaCyc, manually curated and validated specifically for the Solanaceae family and Nicotiana genus, respectively. The curated data have been propagated to the respective Nicotiana-specific databases, which resulted in the enrichment and more accurate presentation of their metabolic networks. The quality and coverage in those databases have been compared with related external databases and discussed in terms of literature support and metabolic content.

Ancestral segmental duplication in Solanaceae is responsible for the origin of CRCa-CRCb paralogues in the family.

CRABS CLAW (CRC), a member of YABBY transcription factor family, has been previously reported to be principally involved in carpel development across angiosperms, and nectary development in core eudicots. Most of the studies suggest that CRC exists as a single copy gene, except in the Solanaceae where CRC occurs as paralogous pairs-CRCa-CRCb in Solanum lycopersicum, and CRC1-CRC2 in Petunia hybrida. In spite of their crucial role in carpel and nectary development, there is no information about the evolutionary history of the CRC paralogy in Solanaceae and whether the paralogy extends beyond Solanaceae. We analyzed homologues of CRC across angiosperms including genome sequence of fourteen species of Solanaceae available at Sol Genomics Network database, Phytozome and NCBI, to address the questions. Our phylogenetic reconstruction across angiosperms combined with comparative genomic, microsynteny and genome-fractionation analyses across the Solanaceae genomes revealed that (1) the CRCa-CRCb lineage is represented by a single copy in other flowering plants; (2) putative homologues of CRCa and CRCb are present in all the Solanaceae genomes studied; (3) the CRCa-CRCb paralogy in Solanaceae is associated with a large segmental duplication within Solanaceae (perhaps in its common ancestor), and (4) the duplicated segments have undergone different degrees of retention and loss of genes. Also, the CRC gene lineage expanded in Solanaceae following Solanaceae-α hexaploidy event and that two CRC duplicate copies were subsequently retained during the course of evolution. Besides the first detailed description of CRC evolution in Solanaceae, the study identifies potential candidate genes for future functional investigations.

In silico identification and characterization of starch synthase (SS) genes in potato (Solanum tuberosum)

Starch is the major source of storage carbohydrate, which is important product for plant and animal as well as for industrial use. Starch synthase (SS) enzyme encoded by several genes is the key factors in starch biosynthetic pathway. Genome wide exploration and characterization of these starch synthase (SS) genes are still limited in the literature. Therefore, intensive bioinformatic tools were approached to identify and in silico characterize the SS genes in potato genome. We identified several orthologues of SS in Arabidopsis by using the term starch synthase in Arabidopsis genome database (TAIR) and National Centre for Biotechnology Information (NCBI). These orthologues were blast in Sol Genomics network and ten SS genes were confirmed as member of the family following Hidden Markov Model (HMM). The genes were characterized in silico for chromosomal locations, phylogeny, exon-intron, domains and motif content, molecular weight and nature of proteins and predicted the functions using different online bioinformatic tools. Chromosomal map and phylogenetic tree were constructed for analyzing evolutionary pattern and relationship with the SS genes of other crop species. The SS genes are distributed on 4 chromosomes (chromosome number 2, 3, 7 and 8) out of 12 potato basic chromosomes and originated from Arabidopsis. The results of this study will be provided basic information in planning future research regarding the regulatory mechanism of search synthesis both under normal and stress condition.

SolCyc: a database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks in Solanum and Nicotiana specific databases.

SolCyc is the entry portal to pathway/genome databases (PGDBs) for major species of the Solanaceae family hosted at the Sol Genomics Network. Currently, SolCyc comprises six organism-specific PGDBs for tomato, potato, pepper, petunia, tobacco and one Rubiaceae, coffee. The metabolic networks of those PGDBs have been computationally predicted by the pathologic component of the pathway tools software using the manually curated multi-domain database MetaCyc (http://www.metacyc.org/) as reference. SolCyc has been recently extended by taxon-specific databases, i.e. the family-specific SolanaCyc database, containing only curated data pertinent to species of the nightshade family, and NicotianaCyc, a genus-specific database that stores all relevant metabolic data of the Nicotiana genus. Through manual curation of the published literature, new metabolic pathways have been created in those databases, which are complemented by the continuously updated, relevant species-specific pathways from MetaCyc. At present, SolanaCyc comprises 199 pathways and 29 superpathways and NicotianaCyc accounts for 72 pathways and 13 superpathways. Curator-maintained, taxon-specific databases such as SolanaCyc and NicotianaCyc are characterized by an enrichment of data specific to these taxa and free of falsely predicted pathways. Both databases have been used to update recently created Nicotiana-specific databases for Nicotiana tabacum, Nicotiana benthamiana, Nicotiana sylvestris and Nicotiana tomentosiformis by propagating verifiable data into those PGDBs. In addition, in-depth curation of the pathways in N.tabacum has been carried out which resulted in the elimination of 156 pathways from the 569 pathways predicted by pathway tools. Together, in-depth curation of the predicted pathway network and the supplementation with curated data from taxon-specific databases has substantially improved the curation status of the species–specific N.tabacum PGDB. The implementation of this strategy will significantly advance the curation status of all organism-specific databases in SolCyc resulting in the improvement on database accuracy, data analysis and visualization of biochemical networks in those species.Database URL https://solgenomics.net/tools/solcyc/

Transcriptome profiling of tobacco (Nicotiana tabacum) pollen and pollen tubes

BackgroundPollen tube growth is essential for plant reproduction and represents a widely employed model to investigate polarized cell expansion, a process important for plant morphogenesis and development. Cellular and regulatory mechanisms underlying pollen tube elongation are under intense investigation, which stands to greatly benefit from a comprehensive understanding of global gene expression profiles in pollen and pollen tubes. Here, RNA sequencing technology was applied to de novo assemble a Nicotiana tabacum male gametophytic transcriptome and to compare transcriptome profiles at two different stages of gametophyte development: mature pollen grains (MPG) and pollen tubes grown for six hours in vitro (PT6).ResultsDe novo assembly of data obtained by 454 sequencing of a normalized cDNA library representing tobacco pollen and pollen tube mRNA (pooled mRNA isolated from mature pollen grains [MPG] and from pollen tubes grown in vitro for 3 [PT3] or 6 [PT6] hours) resulted in the identification of 78,364 unigenes. Among these unigenes, which mapped to 24,933 entries in the Sol Genomics Network (SGN) N. tabacum unigene database, 24,672 were predicted to represent full length cDNAs. In addition, quantitative analyses of data obtained by Illumina sequencing of two separate non-normalized MPG and PT6 cDNA libraries showed that 8979 unigenes were differentially expressed (differentially expressed unigenes: DEGs) between these two developmental stages at a FDR q-value of <0.0001. Interestingly, whereas most of these DEGs were downregulated in PT6, the minor fraction of DEGs upregulated in PT6 was enriched for GO (gene ontology) functions in pollen tube growth or fertilization.ConclusionsA major output of our study is the development of two different high-quality databases representing the tobacco male gametophytic transcriptome and containing encompassing information about global changes in gene expression after pollen germination. Quantitative analyses of these databases 1) indicated that roughly 30% of all tobacco genes are expressed in the male gametophyte, and 2) support previous observations suggesting a global reduction of transcription after pollen germination. Interestingly, a small number of genes, many of which predicted to function in pollen tube growth or fertilization, were found to be upregulated in elongating pollen tubes despite globally reduced transcription.

Characterization and phylogenetic analysis of fifteen NtabSPL genes in Nicotiana tabacum L. cv. Qinyan95.

Fifteen SPL (SQUAMOSA PROMOTER BINDING PROTEIN-LIKE) genes were identified and characterized in Nicotiana tabacum L. cv. Qinyan95. The exon-intron structures of these genes were determined according to the coding sequences confirmed by RT-PCR and the genomic DNA sequences downloaded from the databases in Sol Genomics Network, and thirteen of them were found to carry the response element of miR156. To elucidate the origin of the validated NtabSPL genes, multiple alignments of the nucleotide sequences encompassing the open reading frames were conducted by using the orthologs in N. tabacum, Nicotiana sylvestris, Nicotiana tomentosiformis, and Nicotiana otophora. The results showed that six NtabSPL genes were derived from a progenitor of N. sylvestris, and nine NtabSPL genes were derived from a progenitor of N. tomentosiformis, further corroborating that N. tabacum came from the interspecific hybridization between the ancestors of N. sylvestris and N. tomentosiformis. In contrast to previous statements about highly repetitive sequences, the genome of N. tabacum mainly retained the paternal-derived SPL genes in diploidization process. Phylogenetic analyses based on the highly conserved SBP (SQUAMOSA PROMOTER BINDING PROTEIN) domains and the full-length amino acid sequences reveal that the SPL proteins of tobacco, tomato, and Arabidopsis can be categorized into eight groups. It is worth noting that N. tabacum contains seven NtabSPL6 genes originated from two parental genomes and NtabSPL6-2 possesses a GC-AG intron. In addition, transgenic tobacco plants harboring Arabidopsis Pri-miR156A were generated by Agrobacterium-mediated transformation method, and the constitutive expression of miR156 could obviously inhibit the activity of the NtabSPL genes containing its target site, suggesting the function of miR156 is conservative in tobacco and Arabidopsis.

A set of PCR-based markers for management of a library of Solanum lycopersicoides introgression lines

SummaryA collection of introgression lines (ILs) of Solanum lycopersicoides Dunal in the genetic background of cultivated tomato (S. lycopersicum L.) is a valuable tool for tomato breeding. Efficient management of the collection requires the use of molecular markers. The objective of this work was to identify polymerase chain reaction (PCR)-based markers that were polymorphic between the parents of the ILs, namely ‘VF36’ and ‘LA2951’. In total, 81 primer pairs were tested on genomic DNA from both parents. Genomic DNA of the inter-specific hybrid between the two parents, from which the IL collection had been derived, was also tested. The markers used were either cleaved amplified polymorphic sequence (CAPS) markers or were derived from a set of conserved orthologous genes. In both cases, the markers had been mapped in tomato and described in the SOL Genomics Network. Forty-seven of the markers tested produced a single PCR product in ‘VF36’ and ‘LA2951’. Eleven markers revealed polymorphisms as differences in band-sizes between the two parents. At least one restriction enzyme that generated polymorphism was identified in 29 of the remaining 36 markers. Among other applications, some of these markers have been used to identify plants carrying a target DNA fragment among segregating generations, or to delimit the length of an introgressed sequence.

The Sol Genomics Network (SGN)--from genotype to phenotype to breeding.

The Sol Genomics Network (SGN, http://solgenomics.net) is a web portal with genomic and phenotypic data, and analysis tools for the Solanaceae family and close relatives. SGN hosts whole genome data for an increasing number of Solanaceae family members including tomato, potato, pepper, eggplant, tobacco and Nicotiana benthamiana. The database also stores loci and phenotype data, which researchers can upload and edit with user-friendly web interfaces. Tools such as BLAST, GBrowse and JBrowse for browsing genomes, expression and map data viewers, a locus community annotation system and a QTL analysis tools are available. A new tool was recently implemented to improve Virus-Induced Gene Silencing (VIGS) constructs called the SGN VIGS tool. With the growing genomic and phenotypic data in the database, SGN is now advancing to develop new web-based breeding tools and implement the code and database structure for other species or clade-specific databases.

Transcriptomic analysis of Petunia hybrida in response to salt stress using high throughput RNA sequencing.

Salinity and drought stress are the primary cause of crop losses worldwide. In sodic saline soils sodium chloride (NaCl) disrupts normal plant growth and development. The complex interactions of plant systems with abiotic stress have made RNA sequencing a more holistic and appealing approach to study transcriptome level responses in a single cell and/or tissue. In this work, we determined the Petunia transcriptome response to NaCl stress by sequencing leaf samples and assembling 196 million Illumina reads with Trinity software. Using our reference transcriptome we identified more than 7,000 genes that were differentially expressed within 24 h of acute NaCl stress. The proposed transcriptome can also be used as an excellent tool for biological and bioinformatics in the absence of an available Petunia genome and it is available at the SOL Genomics Network (SGN) http://solgenomics.net. Genes related to regulation of reactive oxygen species, transport, and signal transductions as well as novel and undescribed transcripts were among those differentially expressed in response to salt stress. The candidate genes identified in this study can be applied as markers for breeding or to genetically engineer plants to enhance salt tolerance. Gene Ontology analyses indicated that most of the NaCl damage happened at 24 h inducing genotoxicity, affecting transport and organelles due to the high concentration of Na+ ions. Finally, we report a modification to the library preparation protocol whereby cDNA samples were bar-coded with non-HPLC purified primers, without affecting the quality and quantity of the RNA-seq data. The methodological improvement presented here could substantially reduce the cost of sample preparation for future high-throughput RNA sequencing experiments.

Linking the potato genome to the conserved ortholog set (COS) markers

BackgroundConserved ortholog set (COS) markers are an important functional genomics resource that has greatly improved orthology detection in Asterid species. A comprehensive list of these markers is available at Sol Genomics Network (http://solgenomics.net/) and many of these have been placed on the genetic maps of a number of solanaceous species.ResultsWe amplified over 300 COS markers from eight potato accessions involving two diploid landraces of Solanum tuberosum Andigenum group (formerly classified as S. goniocalyx, S. phureja), and a dihaploid clone derived from a modern tetraploid cultivar of S. tuberosum and the wild species S. berthaultii, S. chomatophilum, and S. paucissectum. By BLASTn (Basic Local Alignment Search Tool of the NCBI, National Center for Biotechnology Information) algorithm we mapped the DNA sequences of these markers into the potato genome sequence. Additionally, we mapped a subset of these markers genetically in potato and present a comparison between the physical and genetic locations of these markers in potato and in comparison with the genetic location in tomato. We found that most of the COS markers are single-copy in the reference genome of potato and that the genetic location in tomato and physical location in potato sequence are mostly in agreement. However, we did find some COS markers that are present in multiple copies and those that map in unexpected locations. Sequence comparisons between species show that some of these markers may be paralogs.ConclusionsThe sequence-based physical map becomes helpful in identification of markers for traits of interest thereby reducing the number of markers to be tested for applications like marker assisted selection, diversity, and phylogenetic studies.

From manual curation to visualization of gene families and networks across Solanaceae plant species

High-quality manual annotation methods and practices need to be scaled to the increased rate of genomic data production. Curation based on gene families and gene networks is one approach that can significantly increase both curation efficiency and quality. The Sol Genomics Network (SGN; http://solgenomics.net) is a comparative genomics platform, with genetic, genomic and phenotypic information of the Solanaceae family and its closely related species that incorporates a community-based gene and phenotype curation system. In this article, we describe a manual curation system for gene families aimed at facilitating curation, querying and visualization of gene interaction patterns underlying complex biological processes, including an interface for efficiently capturing information from experiments with large data sets reported in the literature. Well-annotated multigene families are useful for further exploration of genome organization and gene evolution across species. As an example, we illustrate the system with the multigene transcription factor families, WRKY and Small Auxin Up-regulated RNA (SAUR), which both play important roles in responding to abiotic stresses in plants.Database URL: http://solgenomics.net/

A Draft Genome Sequence ofNicotiana benthamianato Enhance Molecular Plant-Microbe Biology Research

Nicotiana benthamiana is a widely used model plant species for the study of fundamental questions in molecular plant-microbe interactions and other areas of plant biology. This popularity derives from its well-characterized susceptibility to diverse pathogens and, especially, its amenability to virus-induced gene silencing and transient protein expression methods. Here, we report the generation of a 63-fold coverage draft genome sequence of N. benthamiana and its availability on the Sol Genomics Network for both BLAST searches and for downloading to local servers. The estimated genome size of N. benthamiana is 3 Gb (gigabases). The current assembly consists of approximately 141,000 scaffolds, spanning 2.6 Gb with 50% of the genome sequence contained within scaffolds >89 kilobases. Of the approximately 16,000 N. benthamiana unigenes available in GenBank, >90% are represented in the assembly. The usefulness of the sequence was demonstrated by the retrieval of N. benthamiana orthologs for 24 immunity-associated genes from other species including Ago2, Ago7, Bak1, Bik1, Crt1, Fls2, Pto, Prf, Rar1, and mitogen-activated protein kinases. The sequence will also be useful for comparative genomics in the Solanaceae family as shown here by the discovery of microsynteny between N. benthamiana and tomato in the region encompassing the Pto and Prf genes.

분자마커 이용 여교잡 육종을 위한 토마토 유전자원 평가 및 SSR 마커 개발

This study was conducted to achieve basal information for the development of tomato cultivars with disease resistances through marker-assisted backcross (MAB). Ten inbred lines with TYLCV, late blight, bacterial wilt, or powdery mildew resistance and four adapted inbred lines with superior horticultural traits were collected, which can be useful as the donor parents and recurrent parents in MAB, respectively. Inbred lines collected were evaluated by molecular markers and bioassay for confirming their disease resistances. To develop DNA markers for selecting recurrent parent genome (background selection) in MAB, a total of 108 simple sequence repeat (SSR) primer sets (nine per chromosome at average) were selected from the tomato reference genetic maps posted on SOL Genomics Network. Genetic similarity and relationships among the inbred lines were assessed using a total of 303 polymorphic SSR markers. Similarity coefficient ranged from 0.33 to 0.80; the highest similarity coefficient (0.80) was found between bacterial wilt-resistant donor lines ‘10BA333’ and ‘10BA424’, and the lowest (0.33) between a late blight resistant-wild species L3708 (S. pimpinelliforium L.) and ‘10BA424’. UPGMA analysis grouped the inbred lines into three clusters based on the similarity coefficient 0.58. Most of the donor lines of the same resistance were closely related, indicating the possibility that these lines were developed using a common resistance source. Parent combinations (donor parent × recurrent parent) showing appropriate levels of genetic distance and SSR marker polymorphism for MAB were selected based on the dendrogram. These combinations included ‘TYR1’ × ‘RPL1’ for TYLCV, ‘10BA333’ or ‘10BA424’ × ‘RPL2’ for bacterial wilt, and ‘KNU12’ × ‘AV107-4’ or ‘RPL2’ for powdery mildew. For late blight, the wild species resistant line ‘L3708’ was distantly related to all recurrent parental lines, and a suitable parent combination for MAB was ‘L3708’ × ‘AV107-4’, which showed a similarity coefficient of 0.41 and 45 polymorphic SSR markers.

The plant genome: an evolutionary perspective on structure and function

The plant genome: an evolutionary perspective on structure and function

Construction of a potato consensus map and QTL meta-analysis offer new insights into the genetic architecture of late blight resistance and plant maturity traits

BackgroundIntegrating QTL results from independent experiments performed on related species helps to survey the genetic diversity of loci/alleles underlying complex traits, and to highlight potential targets for breeding or QTL cloning. Potato (Solanum tuberosum L.) late blight resistance has been thoroughly studied, generating mapping data for many Rpi-genes (R-genes to Phytophthora infestans) and QTLs (quantitative trait loci). Moreover, late blight resistance was often associated with plant maturity. To get insight into the genomic organization of late blight resistance loci as compared to maturity QTLs, a QTL meta-analysis was performed for both traits.ResultsNineteen QTL publications for late blight resistance were considered, seven of them reported maturity QTLs. Twenty-one QTL maps and eight reference maps were compiled to construct a 2,141-marker consensus map on which QTLs were projected and clustered into meta-QTLs. The whole-genome QTL meta-analysis reduced by six-fold late blight resistance QTLs (by clustering 144 QTLs into 24 meta-QTLs), by ca. five-fold maturity QTLs (by clustering 42 QTLs into eight meta-QTLs), and by ca. two-fold QTL confidence interval mean. Late blight resistance meta-QTLs were observed on every chromosome and maturity meta-QTLs on only six chromosomes.ConclusionsMeta-analysis helped to refine the genomic regions of interest frequently described, and provided the closest flanking markers. Meta-QTLs of late blight resistance and maturity juxtaposed along chromosomes IV, V and VIII, and overlapped on chromosomes VI and XI. The distribution of late blight resistance meta-QTLs is significantly independent from those of Rpi-genes, resistance gene analogs and defence-related loci. The anchorage of meta-QTLs to the potato genome sequence, recently publicly released, will especially improve the candidate gene selection to determine the genes underlying meta-QTLs. All mapping data are available from the Sol Genomics Network (SGN) database.

WebWatch

BioTechniquesVol. 50, No. 1 WebWatchOpen AccessWebWatchKevin AhernKevin AhernSearch for more papers by this authorPublished Online:28 Jun 2018https://doi.org/10.2144/000113583AboutSectionsPDF/EPUB ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinkedInReddit Directed CurrentsStaying current with scientific literature is a must for research scientists, but there is more to it than just reading journals. Helping both scientists and nonscientists see the “forest” of biology for its individual “trees” is biologynews.net, an up-to-the-minute news service focusing on fast-breaking coverage of the biological sciences. The opening page of the site has teaser headlines with a sentence or two of introduction and links to full articles. A lot of information is jammed into a relatively small space using this format, leaving the visitor with a lot of options. The site averages 2000 article views per day. Information is available in RSS feeds and the code is provided for streaming headlines across visitors’ own web sites.[www.biologynews.net]The Soul of SolanaceaeEconomically it's the third most important plant taxon—containing over 3000 species that evolved in the Andean/Amazonian areas of South America—and it contains the most variety of crops in terms of agricultural utility. Some grow above ground, others below. Some are delicious. Others are deadly poisonous. There are reports they may also be linked to cancer. The group is the Solanaceae family, which includes tomatoes, potatoes, eggplants, peppers, and even tobacco. Gathering up and reporting information about this diverse collection of species is the Sol Genomics Network, which keeps visitors abreast of genomic developments, phenoltypes, relevant genes, pathways. It even has a section for plant breeders.[http://solgenomics.net]Population BombForget nuclear bombs, the ozone hole, bioterrorism, or an economic meltdown. The greatest danger to a healthy Earth is the population bomb. At least that's what a growing number of endorsers of the message at Global Population Speak Out are poised to say. The web site reveals a ticking count of humans on Earth in real time and it's a bit unsettling. The designers of the site suggest the size of the human population is the root of environmental problems, and they have a plan for making the public more aware of the problem. During February 2011, a planet wide Speak Out about the problem is being organized. Professionals and concerned visitors can sign up to participate.[www.populationspeakout.org]The Nature of Mother NatureJolle Jolles is a young scientist who brings his love of “our weird and fascinating natural world” to everyone in the form of an interesting set of pages known as Mudfooted.com. He is also a prime example of how a diverse upbringing can lead to great things. Jolles's self-described journey through life, with world travels that include stops in the Netherlands, New Zealand, and Australia, field work in Borneo and South Africa, and time at Cambridge University is mirrored in his delightful web site. The highlight of the site just might be its collection of the most jaw-dropping wildlife videos to be found anywhere on the Web. Here visitors will discover the Jesus Christ lizard (walks on water), Bob (the fish that loves to be petted), and the intelligent use of tools by birds. Thirteen pages of videos and an interesting article archive await curiosity seekers.[http://mudfooted.com]A proboscis monkey jumping over a river.© 2010 by J. Jolles, www.mudfooted.com.PhosphotargetingProtein phosphorylation is a fairly simple phenomenon. The product of action of a kinase, the process adds phosphate to a protein's amino acids with hydroxyl side chains. These, of course, include serine, threonine, and tyrosine. The problem, though, is that there are many such residues in any given polypeptide and not every one of them is acted on. What, then, is the target of the kinases? That's the $64,000 question that Scansite attempts to answer. Tools to determine kinase targets include Motif scans of input or database sequences, database searches using a given motif, sequence pattern matches, and simple protein info determination (molecular weight, pI, and amino acid composition around known phosphorylation sites).[http://scansite.mit.edu]Tech TextingDavid Bradley is a self-described “science communicator since 1989,” who aims with his web site to (i) improve science literacy and numeracy in the media and (ii) encourage streaming, blogging and browsing for other science bloggers by revealing computing tricks and hacks he has uncovered in the process of running his site. In furtherance of his goals, David's insightful views on technology, science, and other topics abound. Indeed, the amount of writing, editing, and collecting he does on a daily basis to stay on top of his site is impressive. If you want a refreshing perspective focused on techno-biology, this is the place to find it.[www.sciencetext.com]FiguresReferencesRelatedDetails Vol. 50, No. 1 Follow us on social media for the latest updates Metrics History Published online 28 June 2018 Published in print January 2011 Information© 2011 Author(s)PDF download

SolQTL: a tool for QTL analysis, visualization and linking to genomes at SGN database

BackgroundA common approach to understanding the genetic basis of complex traits is through identification of associated quantitative trait loci (QTL). Fine mapping QTLs requires several generations of backcrosses and analysis of large populations, which is time-consuming and costly effort. Furthermore, as entire genomes are being sequenced and an increasing amount of genetic and expression data are being generated, a challenge remains: linking phenotypic variation to the underlying genomic variation. To identify candidate genes and understand the molecular basis underlying the phenotypic variation of traits, bioinformatic approaches are needed to exploit information such as genetic map, expression and whole genome sequence data of organisms in biological databases.DescriptionThe Sol Genomics Network (SGN, http://solgenomics.net) is a primary repository for phenotypic, genetic, genomic, expression and metabolic data for the Solanaceae family and other related Asterids species and houses a variety of bioinformatics tools. SGN has implemented a new approach to QTL data organization, storage, analysis, and cross-links with other relevant data in internal and external databases. The new QTL module, solQTL, http://solgenomics.net/qtl/, employs a user-friendly web interface for uploading raw phenotype and genotype data to the database, R/QTL mapping software for on-the-fly QTL analysis and algorithms for online visualization and cross-referencing of QTLs to relevant datasets and tools such as the SGN Comparative Map Viewer and Genome Browser. Here, we describe the development of the solQTL module and demonstrate its application.ConclusionssolQTL allows Solanaceae researchers to upload raw genotype and phenotype data to SGN, perform QTL analysis and dynamically cross-link to relevant genetic, expression and genome annotations. Exploration and synthesis of the relevant data is expected to help facilitate identification of candidate genes underlying phenotypic variation and markers more closely linked to QTLs. solQTL is freely available on SGN and can be used in private or public mode.